Sequencing of polynucleotides relates to determining the arrangement of individual nucleotides in the polynucleotides. Polynucleotides can include sequences of nucleotides arranged in a linear chain of organic molecules that are nitrogen-containing bases, such as adenine (A), guanine (G), thymine (T), cytosine (C), in the case of deoxyribonucleic acid (DNA) and A, G, C, and uracil (U), in the case of ribonucleic acid (RNA). Polynucleotides can be naturally-occurring or synthetic. In some cases, individual nucleotides included in a polynucleotide can pair with a complementary nucleotide in another polynucleotide to produce a double stranded arrangement of polynucleotides. For example, in the case of DNA, T's and A's are complementary and G's and C's are complementary. In the case of ribonucleic acid (RNA), A's and U's are complementary and G's and C's are complementary.
To determine whether a sequencing machine is operating according to specified parameters, a calibration process can take place. The calibration process can include reading one or more nucleotides in a region of at least a portion of the polynucleotides being sequenced. The region of the polynucleotides used during the calibration process can be referred to herein as a “calibration region.” In situations where errors occur during calibration, the sequencing machine can stop the sequencing process. In some cases, the errors that occur during sequencing are not related to improper functioning of the sequencing machine, but the errors can be related to the polynucleotides being sequenced. Overcoming the problems that occur during the calibration process where the composition of the polynucleotides contribute to errors can introduce efficiencies into the sequencing process.